I am trying to analyze the micro array gene expression data between control and treatment. I would like to use R programming package. Which package is better and how can i use. I want step by step tutorial from you. Please provide the code of specific package, if you have.
Thanks in advance.
Use Bioconductor packages from R. Tutorial found here: https://www.bioconductor.org/packages/devel/workflows/vignettes/maEndToEnd/inst/doc/MA-Workflow.html
Typically questions for bioinformatics are much better suited to Biostars (https://www.biostars.org) or Stack Overflow (https://stackoverflow.com), and it is always a good idea in computational analysis to make a good faith effort to do the analysis yourself before asking the community for help, as there are hundreds of ways to do these analyses and it is difficult to give good advice with such a generic question. Best of luck with the analysis.
This is a very generic question as mentioned since I do not even know which platform you used and what is your raw data format or what is your end goal. Here is a step by step training that I recommend people to go through https://www.ebi.ac.uk/training/online/course/functional-genomics-ii-common-technologies-and-data-analysis-methods/analysis-microarray-data. It is very easy to follow if you have familiarity with genomic data analysis. Good luck!
As mentioned by James above Bioconductor is the place. R-package "limma" is almost the default one. It has a well written manual and vignette in Bioconductor. It is generally accepted and good for publication if you later decided to pubish your findings. It is worth reading the other guides mentioned by Anukana if you are doing it for the first time to have a basic understanding and to avoid pitfalls. Goodluck Nazim.
What is your data set size? If it's more than a few, you can use our machine learning platform to generate a gene signature that can classify control vs. treatment. Our platform is no-code and fully automated (we have a simple 3-step workflow), so no experience/training required. Beta-version is FREE to use/try, just go sign up here https://demo.solvergen.com/accounts/login/
also happy to give you more information if you'd like. hope this helps! -Jane
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